Merge pull request #198 from nf-core/dev

3.1.0 Seductive Siren release

Author: jfy133

.github/workflows/nf-test.yml

@@ -64,6 +64,7 @@ jobs:
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
+      - volume=40gb
     strategy:
       fail-fast: false
       matrix:

.gitignore

@@ -10,3 +10,4 @@ null/
 .lineage/
 .nf-test*
 test.xml
+.vscode/settings.json

.nf-core.yml

@@ -2,7 +2,7 @@ lint:
   files_exist:
     - conf/igenomes.config
     - conf/igenomes_ignored.config
-nf_core_version: 4.0.1
+nf_core_version: 4.0.2
 repository_type: pipeline
 template:
   author: James A. Fellows Yates and the nf-core community
@@ -15,4 +15,4 @@ template:
   skip_features:
     - fastqc
     - igenomes
-  version: 3.0.0
+  version: 3.1.0

CHANGELOG.md

@@ -3,28 +3,47 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v3.1.0 - Seductive Siren - [2026-06-03]
+
+### `Added`
+
+- [#194](https://github.com/nf-core/createtaxdb/pull/194) - Updated to nf-core template 4.0.2 (by @jfy133)
+- [#195](https://github.com/nf-core/createtaxdb/pull/195) - Added Centrifuger database building support (by @haris18s)
+
+### `Fixed`
+
+- [#196](https://github.com/nf-core/createtaxdb/pull/169) - Improved KrakenUniq build clean up step (by @mahesh-panchal, @jfy133)
+
+### `Dependencies`
+
+| Tool             | Old Version | New Version |
+| ---------------- | ----------- | ----------- |
+| nf-core template | 4.0.1       | 4.0.2       |
+| nf-schema        | 2.5.1       | 2.7.2       |
+| Centrifuger      |             | 1.1.0       |
+
 ## v3.0.0 - Mystical Medusa - [2026-04-30]
 
 ### `Added`
 
-- [#169](https://github.com/nf-core/createtaxdb/pull/169) Have KAIJU_MKFMI module also export relevant taxdump files for downstream processes (by @jfy133)
-- [#170](https://github.com/nf-core/createtaxdb/pull/170) Publish sometimes generated `unmapped.txt` file for Kraken2 databases (❤️ to @softstam for reporting, fix @jfy133)
-- [#178](https://github.com/nf-core/createtaxdb/pull/178) Add additional validation checks for required MetaCache inputs (by @jfy133)
-- [#179](https://github.com/nf-core/createtaxdb/pull/179) Add new parameter `--save_uncompressed_fastas` to only optionally save decompressed input files (fix @jfy133)
+- [#169](https://github.com/nf-core/createtaxdb/pull/169) - Have KAIJU_MKFMI module also export relevant taxdump files for downstream processes (by @jfy133)
+- [#170](https://github.com/nf-core/createtaxdb/pull/170) - Publish sometimes generated `unmapped.txt` file for Kraken2 databases (❤️ to @softstam for reporting, fix @jfy133)
+- [#178](https://github.com/nf-core/createtaxdb/pull/178) - Add additional validation checks for required MetaCache inputs (by @jfy133)
+- [#179](https://github.com/nf-core/createtaxdb/pull/179) - Add new parameter `--save_uncompressed_fastas` to only optionally save decompressed input files (fix @jfy133)
 
 ### `Fixed`
 
-- [#158](https://github.com/nf-core/createtaxdb/pull/158) Prevent sylph failing due to too long commands when many input genomes (by @softstam, @jfy133)
-- [#160](https://github.com/nf-core/createtaxdb/pull/160) Prevent sourmash failing due to too long commands when many input genomes (by @softstam, @jfy133)
-- [#161](https://github.com/nf-core/createtaxdb/pull/161) Force METACACHE_BUILD module to always use one CPU, as not multi-threaded, removing warning (by @jfy133)
-- [#162](https://github.com/nf-core/createtaxdb/pull/162) Fix links to FAQ in parameter docs (by @jfy133)
-- [#163](https://github.com/nf-core/createtaxdb/pull/163) Fix code block title in auxiliary files section of FAQ (by @jfy133)
-- [#165](https://github.com/nf-core/createtaxdb/pull/165) Force use of KrakenUniq `--jellyfish-bin` to ensure more regular execution (by @jfy133)
-- [#173](https://github.com/nf-core/createtaxdb/pull/173) Fix generated downstream samplesheet's Bracken directory name being flipped (by @jfy133)
-- [#175](https://github.com/nf-core/createtaxdb/pull/175) Fix MetaCache receiving wrong taxonomy file (was seq2map, should have been accession2taxid) (by @sofstam, @jfy133)
-- [#182](https://github.com/nf-core/createtaxdb/pull/182) KMCP emits correct taxonomy files for downstream use (by @sofstam, @jfy133)
-- [#183](https://github.com/nf-core/createtaxdb/pull/183) Fix KrakenUniq using incorrectly non-renamed seqid2map taxonomy file, resulting in no taxonomy info during classification (by @jfy133)
-- [#184](https://github.com/nf-core/createtaxdb/pull/184) Stop generation of concatenated FASTA file of input files if not needed by selected tools (by @jfy133)
+- [#158](https://github.com/nf-core/createtaxdb/pull/158) - Prevent sylph failing due to too long commands when many input genomes (by @softstam, @jfy133)
+- [#160](https://github.com/nf-core/createtaxdb/pull/160) - Prevent sourmash failing due to too long commands when many input genomes (by @softstam, @jfy133)
+- [#161](https://github.com/nf-core/createtaxdb/pull/161) - Force METACACHE_BUILD module to always use one CPU, as not multi-threaded, removing warning (by @jfy133)
+- [#162](https://github.com/nf-core/createtaxdb/pull/162) - Fix links to FAQ in parameter docs (by @jfy133)
+- [#163](https://github.com/nf-core/createtaxdb/pull/163) - Fix code block title in auxiliary files section of FAQ (by @jfy133)
+- [#165](https://github.com/nf-core/createtaxdb/pull/165) - Force use of KrakenUniq `--jellyfish-bin` to ensure more regular execution (by @jfy133)
+- [#173](https://github.com/nf-core/createtaxdb/pull/173) - Fix generated downstream samplesheet's Bracken directory name being flipped (by @jfy133)
+- [#175](https://github.com/nf-core/createtaxdb/pull/175) - Fix MetaCache receiving wrong taxonomy file (was seq2map, should have been accession2taxid) (by @sofstam, @jfy133)
+- [#182](https://github.com/nf-core/createtaxdb/pull/182) - KMCP emits correct taxonomy files for downstream use (by @sofstam, @jfy133)
+- [#183](https://github.com/nf-core/createtaxdb/pull/183) - Fix KrakenUniq using incorrectly non-renamed seqid2map taxonomy file, resulting in no taxonomy info during classification (by @jfy133)
+- [#184](https://github.com/nf-core/createtaxdb/pull/184) - Stop generation of concatenated FASTA file of input files if not needed by selected tools (by @jfy133)
 
 ### `Dependencies`
 
@@ -34,7 +53,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-- [#179](https://github.com/nf-core/createtaxdb/pull/179) The pipeline no longer by default saves decompressed input FASTA files (see new `save_uncompressed_fastas` parameter) (@jfy133)
+- [#179](https://github.com/nf-core/createtaxdb/pull/179) - The pipeline no longer by default saves decompressed input FASTA files (see new `save_uncompressed_fastas` parameter) (@jfy133)
 
 ## v2.1.0 - Gracious Goblin - [2026-02-10]
 

CITATIONS.md

@@ -18,6 +18,10 @@
 
   > Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016). Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research, 26(12), 1721–1729. https://doi.org/10.1101/gr.210641.116
 
+- [Centrifuger](https://doi.org/10.1186/s13059-024-03244-4)
+
+  > Song, L., Langmead, B. Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification. Genome Biol 25, 106 (2024). https://doi.org/10.1186/s13059-024-03244-4
+
 - [DIAMOND](https://doi.org/10.1038/nmeth.3176)
 
   > Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1), 59–60. https://doi.org/10.1038/nmeth.3176

README.md

@@ -11,7 +11,7 @@
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.1)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.2)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -36,6 +36,7 @@ The pipeline is designed to be a companion pipeline to [nf-core/taxprofiler](htt
 2. Builds databases for:
    - [Bracken](https://doi.org/10.7717/peerj-cs.104)
    - [Centrifuge](https://doi.org/10.1101/gr.210641.116)
+   - [Centrifuger](https://doi.org/10.1186/s13059-024-03244-4)
    - [DIAMOND](https://doi.org/10.1038/nmeth.3176)
    - [ganon](https://doi.org/10.1093/bioinformatics/btaa458)
    - [Kaiju](https://doi.org/10.1038/ncomms11257)
@@ -105,7 +106,7 @@ For more details about the output files and reports, please refer to the
 
 nf-core/createtaxdb was originally written by James A. Fellows Yates, Sam Wilkinson, Alexander Ramos Díaz, Lili Andersson-Li and the nf-core community.
 
-It has been extended by Moritz Beber (@Midnighter; adding sourmash support).
+It has been extended by Moritz Beber (@Midnighter; adding sourmash support) and Haris Spyridis (@haris18s; adding centrifuger support).
 
 We thank the following people for their extensive assistance in the development of this pipeline: